Over the last century, climate change has impacted the physiology, distribution, and phenology of marine and terrestrial primary producers worldwide. The study of these fluctuations has been hindered due to the complex response of plants to environmental forcing over large spatial and temporal scales. To bridge this gap, we investigated the synchrony in seasonal phenological activity between marine and terrestrial primary producers to environmental and climatic variability across northern Patagonia. We disentangled the effects on the biological activity of local processes using advanced time-frequency analysis and partial wavelet coherence on 15 years (2003–2017) of data from MODIS (Moderate Resolution Imaging Spectroradiometer) onboard the Terra and Aqua satellites and global climatic variability using large-scale climate indices. Our results show that periodic variations in both coastal ocean and land productivity are associated with sea surface temperature forcing over seasonal scales and with climatic forcing over multi-annual (2–4 years) modes. These complex relationships indicate that large-scale climatic processes primarily modulate the synchronous phenological seasonal activity across northern Patagonia, which makes these unique ecosystems highly exposed to future climatic change.